This is indeed a very strange problem. I tried to reproduce on Ubuntu 16.04.2 with a fresh install of R-3.4.0 (compiled from source) but cummeRbund (including AnnotationFilter and all other dependencies) installed without any problems.

Hello, I know I'm not the original poster but I am having the exact same problem on R-3.4.0 with a fresh install of cummeRbund. I also tried installing the dependencies 1 by 1 in the order R told me it needed them (aka when I had an error from a package install because of a missing dependency), but that did not work either. Any help or ideas would be appreciated!